thanks a bunch for your help so far guys, I totally agree that I want to verify back to stock in the future but right now I want to get it ridable and running very well, then next would be electro clean up, then aesthetic stuff
so I traced the mystery brown up towards the headlight cluster and found this genius peace of engineering (disconnected as shown) - (first picture "wires 1")
so it does appear that the brown connects up to the grounds coming from almost all front located lights, blinkers, speedo light, tacho light.
the second picture ("wires 2") shows them splitting off into the headlight, I traced most of them and they are coming from blinkers grounds etc.
would this have caused charging problems? I guess if the blinkers ground straight into their holders that explains why they still work, high beam little blue light has been working fine, speedo and tacho night lights have not.
should I solder this up, ground the end near the reg/ rec assembly, reconnect a new reg rec and see if the charging problems are solved?